<commit_before># External Software

## Enveomics Collection
Rodriguez-R LM, Konstantinidis KT. (2016) The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. [PeerJ Preprints 4:e1900v1](https://doi.org/10.7287/peerj.preprints.1900v1)

## SolexaQA++
<NAME>., <NAME>, and <NAME>. 2010. SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11:485. [Web Link](http://www.biomedcentral.com/1471-2105/11/485)

## Scythe
[Git Hub Repo](https://github.com/vsbuffalo/scythe)

## FastQC
[Link to tool site](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

## IDBA-UD
<NAME>., et al. (2012) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth, Bioinformatics, 28, 1420-1428.

## Prodigal
<NAME>, <NAME>, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010 Mar 8;11(1):119. [Web Link](http://www.biomedcentral.com/1471-2105/11/119)

## Barrnap

## Bedtools

## MyTaxa
<NAME>, <NAME>, <NAME>; MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42 (8): e73. [Web Link](https://doi.org/10.1093/nar/gku169)

## MCL
<NAME>., <NAME>., <NAME>., An efficient algorithm for large-scale detection of protein families, Nucleic Acids Research 30(7):1575-1584 (2002).

## Krona<commit_msg>+docs<commit_after># External Software

## Enveomics Collection

Rodriguez-R LM, Konstantinidis KT. (2016) The enveomics collection: a toolbox
for specialized analyses of microbial genomes and metagenomes.
[PeerJ Preprints 4:e1900v1](https://doi.org/10.7287/peerj.preprints.1900v1)

## SolexaQA++

<NAME>., <NAME>, and <NAME>. 2010. SolexaQA: At-a-glance quality
assessment of Illumina second-generation sequencing data. BMC Bioinformatics
11:485. [Web Link](http://www.biomedcentral.com/1471-2105/11/485).

## Scythe

[GitHub: vsbuffalo/scythe](https://github.com/vsbuffalo/scythe), by
<NAME>.

## FastQC

[Link to tool site](https://www.bioinformatics.babraham.ac.uk/projects/fastqc),
by <NAME>.

## IDBA-UD

<NAME>., et al. (2012) IDBA-UD: a de novo assembler for single-cell and
metagenomic sequencing data with highly uneven depth, Bioinformatics, 28,
1420-1428.

## Prodigal

<NAME>, <NAME>, Locascio PF, Land ML, <NAME>, <NAME>. Prodigal:
prokaryotic gene recognition and translation initiation site identification. BMC
Bioinformatics. 2010 Mar 8;11(1):119.
[Web Link](http://www.biomedcentral.com/1471-2105/11/119).

## Barrnap

[GitHub: tseemann/barrnap](https://github.com/tseemann/barrnap), by <NAME>.

## Bedtools

## MyTaxa

<NAME>, <NAME>, <NAME>; MyTaxa: an
advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic
Acids Res 2014; 42 (8): e73. [Web Link](https://doi.org/10.1093/nar/gku169).

## MCL

<NAME>., <NAME>., <NAME>., An efficient algorithm for
large-scale detection of protein families, Nucleic Acids Research
30(7):1575-1584 (2002).

## Krona
{'fraction_non_alphanumeric': 0.14104234527687295, 'fraction_numerical': 0.0742671009771987, 'mean_word_length': 4.940038684719536, 'pattern_counts': {'":': 0, '<': 32, '<?xml version=': 0, '>': 32, 'https://': 9, 'lorem ipsum': 0, 'www.': 6, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5596526', 'n_tokens_mistral': 1305, 'n_tokens_neox': 1044, 'n_words': 302}