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Goby file formats, framework and tools

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We created this group as a forum to discuss common questions about Goby file formats, tools and software framework (see http://goby.campagnelab.org). Post your questions to developers or other users of Goby. Before posting a new question, please take a moment to search the group to search for answers to a similar question.

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6/27/16

We've released Goby 2.3.6. This release improves the scalability of the local realignment

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We've released Goby 2.3.6. This release improves the scalability of the local realignment

6/27/16

Fabien Campagne

3/2/15

We've released Goby 2.3.5. New Features: - Add a mode to infer sex of samples from data (tested

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We've released Goby 2.3.5. New Features: - Add a mode to infer sex of samples from data (tested

3/2/15

Fabien Campagne, yif...@gmail.com6

10/23/14

Goby 2.3.4.1 released

--(note the flag when converting back to fasta): "--identifier-to-header " That's the

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Goby 2.3.4.1 released

--(note the flag when converting back to fasta): "--identifier-to-header " That's the

10/23/14

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Fabien Campagne

1/23/14

Re: Doubt about vcfsubset mode

Hello, I am copying the Goby forum so that others may find the answer if they encounter a similar

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Re: Doubt about vcfsubset mode

Hello, I am copying the Goby forum so that others may find the answer if they encounter a similar

1/23/14

Fabien Campagne, Dror Kessler2

3/6/13

Re: Update, Short Question

Dear Fabien; Thank you for your response. I hope you had a good time off/vacation. Yes, I have

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Re: Update, Short Question

Dear Fabien; Thank you for your response. I hope you had a good time off/vacation. Yes, I have

3/6/13

Fabien Campagne, … Dror Kessler4

2/17/13

Fwd: goby-framework - Google Groups: Message Pending [{ILGIo4Wexe7_CyoCcWEwARlUTOcvXWvC0}]

Fabien Hi; I understand the semantic fault you are indicating in the input file. We are studying it.

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Fwd: goby-framework - Google Groups: Message Pending [{ILGIo4Wexe7_CyoCcWEwARlUTOcvXWvC0}]

Fabien Hi; I understand the semantic fault you are indicating in the input file. We are studying it.

2/17/13

Fabien Campagne

2/11/13

Fwd: goby-framework - Google Groups: Message Pending [{II6Ih8eGlaCQRyoCcWEwAYljj77Gx6Hu0}]

Forwarded message ---------- From: Dror Kessler <dror.k...@gmail.com> To: goby-framework@

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Fwd: goby-framework - Google Groups: Message Pending [{II6Ih8eGlaCQRyoCcWEwAYljj77Gx6Hu0}]

Forwarded message ---------- From: Dror Kessler <dror.k...@gmail.com> To: goby-framework@

2/11/13

Fabien Campagne

11/29/12

manuscript pre-prints posted to arXiv, VCFParser issue fixed

We have posted the Goby/compression manuscript as a pre-print on arXiv. See http://arxiv.org/abs/

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manuscript pre-prints posted to arXiv, VCFParser issue fixed

We have posted the Goby/compression manuscript as a pre-print on arXiv. See http://arxiv.org/abs/

11/29/12

Fabien Campagne, … Vadim Zalunin14

7/6/12

Re: [Samtools-devel] Goby 2.0 released

On 06/07/2012 14:02, Fabien Campagne wrote: On Thu, Jul 5, 2012 at 1:35 PM, Heng Li <l...@sanger.ac

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Re: [Samtools-devel] Goby 2.0 released

On 06/07/2012 14:02, Fabien Campagne wrote: On Thu, Jul 5, 2012 at 1:35 PM, Heng Li <l...@sanger.ac

7/6/12

Fabien Campagne

6/4/12

We have pushed the second release candidate for Goby 2.0 (2.0RC2). This tutorial describes the key

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We have pushed the second release candidate for Goby 2.0 (2.0RC2). This tutorial describes the key

6/4/12

Fabien Campagne

3/17/12

We have used Goby file formats extensively internally at Weill Cornell to implement all sorts of

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We have used Goby file formats extensively internally at Weill Cornell to implement all sorts of

3/17/12

Fabien Campagne

3/17/12

Released Goby 1.9.8.4.2

Another fix related to converting SAM/BAM to Goby. Please let us know if you find any other issue

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Released Goby 1.9.8.4.2

Another fix related to converting SAM/BAM to Goby. Please let us know if you find any other issue

3/17/12

Fabien Campagne

3/16/12

Release 1.9.8.4.1

We pushed Goby 1.9.8.4.1: - Improve speed of sam-to-compact when log4j is not configured properly. -

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Release 1.9.8.4.1

We pushed Goby 1.9.8.4.1: - Improve speed of sam-to-compact when log4j is not configured properly. -

3/16/12

Fabien Campagne

3/15/12

Goby 1.9.8.4 released (fixes sam-to-compact)

Available from http://campagnelab.org/software/goby/download-goby/ This releases fixes various

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Goby 1.9.8.4 released (fixes sam-to-compact)

Available from http://campagnelab.org/software/goby/download-goby/ This releases fixes various

3/15/12

Fabien Campagne

3/6/12

We have created a number of tutorials to describe how to use Goby for various types of projects.

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We have created a number of tutorials to describe how to use Goby for various types of projects.

3/6/12

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