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Resources marked with > are used, have been used, or are actively advocated in the threads. This applies for everything in the [Necessities] section.
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[Necessities]
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Hiragana & Katakana: http://www.realkana.com/ OR
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Remembering the Kana: https://anonfiles.com/file/096e5b285b874c9bf0f83d7094e0e81d
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Kanji: http://kanjidamage.com/
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Japanese IME: http://www.google.com/intl/ja/ime/
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Anki Flashcards: http://ankisrs.net/
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Genki (↓Bottom↓)
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Tae Kim Japanese: http://www.guidetojapanese.org/learn/grammar
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http://rikaisama.sourceforge.net/ (Firefox only)
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[Websites]
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http://japanese.stackexchange.com/
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https://www.erin.ne.jp/en/lesson01/basic/index.html (video + script)
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http://www.yomiuri.co.jp/dy/columns/0002/ (column of short Japanese lessons)
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http://www.imabi.net/ (grammar)
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http://en.wikipedia.org/wiki/Japanese_grammar (surprisingly comprehensive and useful)
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http://www.memrise.com/ (basically anki with flowers and other neat and colour features and methods)
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[Grammar]
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>http://www.guidetojapanese.org/ (Tae Kim) (Site seems to be down quite often so you might want to download this http://www.mediafire.com/download/hq2536ew6anf5wt/grammar_guide.pdf)
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http://www.csse.monash.edu.au/~jwb/j_gram_summ.html
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http://www.jekai.org/
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http://www.geocities.jp/niwasaburoo/index.html - Book on Japanese grammar, written in Japanese
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http://www.hello-school.net/hsjap.htm
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http://en.wikibooks.org/wiki/Japanese/Grammar
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http://kimallen.sheepdogdesign.net/Japanese/index.html
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http://www.jgram.org/ - jgram has not updated to the new JLPT levels yet, but the grammar hasn't changed.
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http://www.tanos.co.uk/jlpt/skills/grammar/
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http://it.scribd.com/doc/6579312/A-Dictionary-of-Japanese-Particles
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http://ww8.tiki.ne.jp/~tmath/home/index.htm
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Yōkouso!	http://www.mediafire.com/?rewg4tx4wte4bxv udp://tracker.openbittorrent.com:80
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>http://thepiratebay.sx/torrent/5892518/Japanese_the_manga_way.pdf (Japanese The Manga Way)
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[Helpful Forums]:
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http://www.guidetojapanese.org/forum/
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http://thejapanesepage.com/
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[Kanji]
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http://kanji.koohii.com/learnmore
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>http://kanji.sljfaq.org/ - Look up kanji through stroke order.
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http://www.asahi-net.or.jp/~ik2r-myr/kanji/listjouyou_en.htm
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http://kakijun.main.jp/ (stroke order)
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https://docs.google.com/spreadsheet/ccc?key=0AuzSRjg-3K_vck9HZmp5YmVkMXJHMDRpMmU2UzFWVkE#gid=0 - A list of the 3622 most common Kanji characters found in the Japanese Wikipedia, along with their frequencies.
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http://www.mediafire.com/?n0nj66yyj7dsqyz - Collection of images from the threads. This link should contain around a 3000 or so kanji. A few images may or may not be missing. Be careful of blunders I might have made as well. If you would like for this to be updated simply ask.
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https://mega.co.nz/#!08NiWI4C!KzBPdt9odA_tMLbHRocpEO9bYQpKOt8G4y19VKvLeu4 - Slime Forest
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[Listening Practice]
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http://www.njuku.com/
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http://jclab.wordpress.com/
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http://hukumusume.com/douwa/pc/minwa/
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http://www.simulradio.jp/
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[Online Dictionaries/Thesauruses]
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http://dic.yahoo.co.jp/
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>http://dic.nicovideo.jp/
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>Good for slang.
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>http://kotobank.jp/
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Good for your rarer words and terms.
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http://dictionary.goo.ne.jp/
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>http://tangorin.com/
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>Provides example sentences along with other common dictionary features.
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>http://www.alc.co.jp/ - Example sentences
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http://zokugo-dict.com/ (general slang)
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http://www.geocities.jp/tomomi965/index2.html (for idioms/set phrases)
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http://www.media-k.co.jp/jiten/ (for 2ch slang/memes/catch phrases)
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http://dbms.kokken.go.jp/nknet/Onomatope/category.html (onomatopoeia)
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http://www.rondely.com/zakkaya/dic5/index.htm (onomatopoeia)
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http://home.alc.co.jp/db/owa/s_kaydic?ctg_in=4 (onomatopoeia)
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http://gogen-allguide.com/ (word etymology)
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http://kanji.reader.bz/ (kanji readings, works for names too)
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http://www016.upp.so-net.ne.jp/hougenn/ (for different Japanese dialects)
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>http://www.weblio.jp/
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[Other]
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>http://lang-8.com/ - (Practice Japanese by writing short passages, receive and give corrections from and to native Japanese speakers)
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http://japanese-speedtest.10fastfingers.com/
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http://lazunin.com/kage_en.html
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ttp://www.start-point.net/nihontizu/ - Prefecture Names
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http://iteslj.org/v/j/ (Vocab  Quizzes)
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http://www.offbeatband.com/2010/12/the-most-commonly-used-japanese-words-by-frequency/
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http://www.csse.monash.edu.au/~jwb/wwwjdicinf.html#code_tag - Info on tags that rikai uses.
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>http://www.supermemo.com/articles/20rules.htm (Interesting article on learning. Recommended Reading, especially if you're wondering how you should set up your decks and so forth.)
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http://www.mediafire.com/?dckt6ix32l93f35 (Collection of the Nihonshock cheatsheets in pdf format.)
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>http://kanjitomo.com/ - 「KanjiTomo is a program for identifying Japanese characters from images」
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http://lapapps.net/ (Kanji for Games, that is, Game X's kanji.)
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http://sukebei.nyaa.eu/?page=torrentinfo&tid=23370 - JapanesePod
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http://gloss.dliflc.edu/Default.aspx 
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http://pastebin.com/xUufY26D - Small pastebin of some resources. Used to be in the Op.
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https://docs.google.com/document/d/17RFFCYPGS9e4YjqkyF2d7W8N787xihdORn_TNHZzCgQ/edit?usp=sharing List proper way of pronouncing kana, using common English words. 
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[Reading and/or Watching]
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https://docs.google.com/spreadsheet/lv?key=0Agk2IH0ZXhn7dDNmSW1BVFU5dVgyOHkzWjU4b2l2dkE&pli=1
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>A reading list made by a kind anon from these threads, and for these threads. Be sure to add stuff you're reading in here.
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http://www.portals.co.jp/isopp/
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http://www.mediafire.com/?93atzwak7dx47- a Mediafire of documents and raw manga to get you started with reading
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http://chokochoko.wordpress.com/the-great-library/
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http://www.j-comi.jp/
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>A Japanese website that provides free (older) manga to read. Mostly tons of old stuff, but it has the entire set of Love Hina (http://www.j-comi.jp/book/comic/1) volumes, which is a pretty entertaining series. 
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http://amaterasu.tindabox.net/guide/j-comi.php
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>This takes a few dozen pages of actual manga, takes apart every single sentence and shows you how to translate them
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http://www.fengyunzhibo.com/space/japan.htm (Chinese site with Japanese television stations. Good quality as well.)
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http://www.jcafe24.net/index.php
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>Another source for manga. You have to set up an account and make a post on one of their forums before you can access the Winny Club, which is where the raw manga is.
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>http://kitsunekko.net/subtitles/japanese/
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>Japanese subtitles for a ton of different anime shows. The only problem is that some of the subs seemed to be timed wrong when used with common raws (Ex: the Japanese subs are set for a 24 minute episode, while the raw is 22 minutes). So you might have to open them up with a subtitle editor and change the times. Regardless, you can usually use these subs with the anime you already have, just disable English subs and load the Japanese subs. For the anime subs, it's worth looking into using a text hooker to extract the text to make it easy to paste into Anki or a dictionary. (Such as AGTH)
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http://www.livingjapanese.com/p/reading-pack.html
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http://www.mediafire.com/download/rzigb3zrcdta35p/Reading+pack+1+and+2.zip
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>Yotsuba Reading pack. First is the official page it came from, and the second link is a download for both reading packs made.	
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http://www.raw1st.org/
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http://www.portals.co.jp/isopp/
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http://rawcs.blogspot.co.il/p/manga-index.html
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http://www.rawmangaspot.com/
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http://www.raw-manga.net/
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http://rawscans.com/
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http://shareraws.blogspot.co.il/
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http://crazy-cake.blogspot.co.il/p/homepage.html
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http://mangahead.com/
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>http://www.aozora.gr.jp/
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[E-Books (PDF)]
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Making Sense of Japanese Grammar (2.56 MB)
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*http://www.mediafire.com/?d8hvs7jyb0fi156
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Japanese Core Words and Phrases (3.79 MB)
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*http://www.mediafire.com/?z1fcbxw4vbnfb2p
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Japanese Particle Workbook (39.2 MB)
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*http://www.mediafire.com/?4c4387dbbg86a43
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Japanese Verbs and Essentials of Grammar (82.1 MB)
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*http://www.mediafire.com/?c3c83or0a5xz2dw
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Japanese Beyond Words (27.1 MB)
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*http://www.mediafire.com/?dcc3yaay9w4fj5c
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Read Real Japanese (80.5 MB)
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*http://www.mediafire.com/?sg2yr34ehldh6ir
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Oxford Japanese Grammar & Verbs (40.1 MB)
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*http://www.mediafire.com/?8xk6v525idpbdb8
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JLPT - Teach Yourself Japanese (32.1 MB)
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*http://www.mediafire.com/?lpwckercaq3mfiw
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(DOJG)
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>Highly recommended resources on the Japanese language. In particular their は and が particle explanations in DOBJG provide particullary useful explanations.
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>Dictionary of Basic Japanese Grammar (24 MB) (DOBJG)
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*http://www.mediafire.com/?c1swbbihl97s77b
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>Dictionary of Intermediate Japanese Grammar (29.6 MB) (DOIJG)
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*http://www.mediafire.com/?7obxdz023iiw3c8
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>Dictionary of Advanced Japanese Grammar (65.4 MB) (DOAJG)
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*http://www.mediafire.com/?r61j67rmntthy9u
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(Genki)
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>Genki I (150.4 MB)
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>*http://www.mediafire.com/?4dsxbexuv92xvuj
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Genki I Workbook (28.6 MB)
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*http://www.mediafire.com/?orjq8jfja8lj4aq
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(Supplemental Audio CDs.)
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Genki I CDs 1 & 2 (102.1 MB)
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*http://www.mediafire.com/?u4ab7xyd2pgi0k7
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Genki I CDs 3 & 4 (118.7 MB)
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*http://www.mediafire.com/?bjzhrte35es2e4z
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Genki I CDs 5 & 6 (119.1 MB)
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*http://www.mediafire.com/?2apq4wv4j2rs9qu
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Genki II (162.4 MB)
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*http://www.mediafire.com/?a2t5giuv35if4gm
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Genki II Workbook (128.7 MB)
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*http://www.mediafire.com/?mm77vpi9731okst
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Genki II CDs 1, 2, & 3 (103.5 MB)
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*http://www.mediafire.com/?6l55tomt2bnhrqq
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Genki II CDs 4, 5, & 6 (95.5 MB)
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*http://www.mediafire.com/?b0m4063od4ghcfm
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Genki I & II Answer Key (65.9 MB)
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*http://www.mediafire.com/?102h82qhflktjdt